18 research outputs found
Thermodynamics of Fragment Binding
The ligand binding pockets of proteins have preponderance
of hydrophobic
amino acids and are typically within the apolar interior of the protein;
nevertheless, they are able to bind low complexity, polar, water-soluble
fragments. In order to understand this phenomenon, we analyzed high
resolution X-ray data of protein–ligand complexes from the
Protein Data Bank and found that fragments bind to proteins with two
near optimal geometry H-bonds on average. The linear extent of the
fragment binding site was found not to be larger than 10 Å, and
the H-bonding region was found to be restricted to about 5 Å
on average. The number of conserved H-bonds in proteins cocrystallized
with multiple different fragments is also near to 2. These fragment
binding sites that are able to form limited number of strong H-bonds
in a hydrophobic environment are identified as hot spots. An estimate
of the free-energy gain of H-bond formation versus apolar desolvation
supports that fragment sized compounds need H-bonds to achieve detectable
binding. This suggests that fragment binding is mostly enthalpic that
is in line with their observed binding thermodynamics documented in
Isothermal Titration Calorimetry (ITC) data sets and gives a thermodynamic
rationale
for fragment based approaches. The binding of larger compounds tends
to more rely on apolar desolvation with a corresponding increase of
the entropy content of their binding free-energy. These findings explain
the reported size-dependence of maximal available affinity and ligand
efficiency both behaving differently in the small molecule region
featured by strong H-bond formation and in the larger molecule region
featured by apolar desolvation
Thermodynamics of Fragment Binding
The ligand binding pockets of proteins have preponderance
of hydrophobic
amino acids and are typically within the apolar interior of the protein;
nevertheless, they are able to bind low complexity, polar, water-soluble
fragments. In order to understand this phenomenon, we analyzed high
resolution X-ray data of protein–ligand complexes from the
Protein Data Bank and found that fragments bind to proteins with two
near optimal geometry H-bonds on average. The linear extent of the
fragment binding site was found not to be larger than 10 Å, and
the H-bonding region was found to be restricted to about 5 Å
on average. The number of conserved H-bonds in proteins cocrystallized
with multiple different fragments is also near to 2. These fragment
binding sites that are able to form limited number of strong H-bonds
in a hydrophobic environment are identified as hot spots. An estimate
of the free-energy gain of H-bond formation versus apolar desolvation
supports that fragment sized compounds need H-bonds to achieve detectable
binding. This suggests that fragment binding is mostly enthalpic that
is in line with their observed binding thermodynamics documented in
Isothermal Titration Calorimetry (ITC) data sets and gives a thermodynamic
rationale
for fragment based approaches. The binding of larger compounds tends
to more rely on apolar desolvation with a corresponding increase of
the entropy content of their binding free-energy. These findings explain
the reported size-dependence of maximal available affinity and ligand
efficiency both behaving differently in the small molecule region
featured by strong H-bond formation and in the larger molecule region
featured by apolar desolvation
How Are Fragments Optimized? A Retrospective Analysis of 145 Fragment Optimizations
Fragment
optimizations in nearly 150 fragment-based drug discovery
programs reported in the literature during the past fifteen years
were investigated. By analyzing physicochemical properties and ligand
efficiency indices we found that biochemical detection methods yield
hits with superior ligand efficiency and lipophilicity indices than
do X-ray and NMR. These advantageous properties are partially preserved
in the optimization since higher affinity starting points allow optimizations
better balanced between affinity and physicochemical property improvements.
Size independent ligand efficiency (SILE) and lipophilic indices (primarily
LELP) were found to be appropriate metrics to monitor optimizations.
Small and medium enterprises (SME) produce optimized compounds with
better properties than do big pharma companies and universities. It
appears that the use of target structural information is a major reason
behind this finding. Structure-based optimization was also found to
dominate successful fragment optimizations that result in clinical
candidates. These observations provide optimization guidelines for
fragment-based drug discovery programs
Discovery of Subtype Selective Janus Kinase (JAK) Inhibitors by Structure-Based Virtual Screening
Janus
kinase inhibitors represent a promising opportunity for the
pharmaceutical intervention of various inflammatory and oncological
indications. Subtype selective inhibition of these enzymes, however,
is still a very challenging goal. In this study, a novel, customized
virtual screening protocol was developed with the intention of providing
an efficient tool for the discovery of subtype selective JAK2 inhibitors.
The screening protocol involves protein ensemble-based docking calculations
combined with an Interaction Fingerprint (IFP) based scoring scheme
for estimating ligand affinities and selectivities, respectively.
The methodology was validated in retrospective studies and was applied
prospectively to screen a large database of commercially available
compounds. Six compounds were identified and confirmed in vitro, with
an indazole-based hit exhibiting promising selectivity for JAK2 vs
JAK1. Having demonstrated that the described methodology is capable
of identifying subtype selective chemical starting points with a favorable
hit rate (11%), we believe that the presented screening concept can
be useful for other kinase targets with challenging selectivity profiles
Comparative Evaluation of Covalent Docking Tools
Increased interest
in covalent drug discovery led to the development
of computer programs predicting binding mode and affinity of covalent
inhibitors. Here we compare the performance of six covalent docking
tools, AutoDock4, CovDock, FITTED, GOLD, ICM-Pro, and MOE, for reproducing
experimental binding modes in an unprecedently large and diverse set
of covalent complexes. It was found that 40–60% of the top
scoring ligand poses are within 2.0 Å RMSD from the experimental
binding mode. This rate showed program dependent increase and achieved
50–90% when the best RMSD among the top ten scoring poses was
considered. This performance is comparable to that of noncovalent
docking tools and therefore suggests that anchoring the ligand does
not necessarily improve the accuracy of the prediction. The effect
of various ligand and protein features on the docking performance
was investigated. At the level of warhead chemistry, higher success
rate was found for Michael additions, nucleophilic additions and nucleophilic
substitutions than for ring opening reactions and disulfide formation.
Increasing ligand size and flexibility generally affects pose predictions
unfavorably, although AutoDock4, FITTED, and ICM-Pro were found to
be less sensitive up to 35 heavy atoms. Increasing the accessibility
of the target cysteine tends to result in improved binding mode predictions.
Docking programs show protein dependent performance suggesting a target-dependent
choice of the optimal docking tool. It was found that noncovalent
docking into Cys/Ala mutated proteins by ICM-Pro and Glide reproduced
experimental binding modes with only slightly lower performance and
at a significantly lower computational expense than covalent docking
did. Overall, our results highlight the key factors influencing the
docking performance of the investigated tools and they give guidelines
for selecting the optimal combination of warheads, ligands, and tools
for the system investigated. Results also identify the most important
aspects to be considered for developing improved protocols for docking
and virtual screening of covalent ligands
Impact of Lipophilic Efficiency on Compound Quality
Lipophilic efficiency indices such as LLE and LELP were
suggested
to support balanced optimization of potency and ADMET profile. Here
we investigated the performance of LLE and LELP on multiple data sets
representing different stages of drug discovery including fragment
and HTS hits and leads, development candidates, phase II compounds,
and launched drugs. Analyzing their impact on ADME and safety properties
and binding thermodynamics, we found that both LLE and LELP help identifying
better quality compounds. LLE is sensible for the development stages
but does not prefer fragment-type hits, while LELP has an advantage
for this class of compounds and discriminates preferred starting points
effectively. Both LLE and LELP have significant impact on ADME and
safety profiles; however, LELP outperforms LLE in risk assessment
at least on the present data set. On the basis of the results reported
here, monitoring lipophilic efficiency metrics could contribute significantly
to compound quality and might improve the output of medicinal chemistry
programs
Multiple Fragment Docking and Linking in Primary and Secondary Pockets of Dopamine Receptors
A sequential docking methodology
was applied to computationally
predict starting points for fragment linking using the human dopamine
D<sub>3</sub> receptor crystal structure and a human dopamine D<sub>2</sub> receptor homology model. Two focused fragment libraries were
docked in the primary and secondary binding sites, and best fragment
combinations were enumerated. Similar top scoring fragments were found
for the primary site, while secondary site fragments were predicted
to convey selectivity. Three linked compounds were synthesized that
had 9-, 39-, and 55-fold selectivity in favor of D<sub>3</sub> and
the subtype selectivity of the compounds was assessed on a structural
basis
Structure-Based Consensus Scoring Scheme for Selecting Class A Aminergic GPCR Fragments
Aminergic G-protein coupled receptors (GPRCs) represent well-known targets of central nervous-system related diseases. In this study a structure-based consensus virtual screening scheme was developed for designing targeted fragment libraries against class A aminergic GPCRs. Nine representative aminergic GPCR structures were selected by first clustering available X-ray structures and then choosing the one in each cluster that performs best in self docking calculations. A consensus scoring protocol was developed using known promiscuous aminergic ligands and decoys as a training set. The consensus score (FrACS-fragment aminergic consensus score) calculated for the optimized protein ensemble showed improved enrichments in most cases as compared to stand-alone structures. Retrospective validation was carried out on public screening data for aminergic targets (5-HT1 serotonin receptor, TA(1) trace-amine receptor) showing 8-17-fold enrichments using an ensemble of aminergic receptor structures. The performance of the structure based FrACS in combination with our ligand-based prefilter (FrAGS) was investigated both in a retrospective validation on the ChEMBL database and in a prospective validation on an in-house fragment library. In prospective validation virtual fragment hits were tested on S-HT6 serotonin receptors not involved in the development of FrACS. Six out of the 36 experimentally tested fragments exhibited remarkable antagonist efficacies, and 4 showed IC50 values in the low micromolar or submicromolar range in a cell-based assay. Both retrospective and prospective validations revealed that the methodology is suitable for designing focused class A GPCR fragment libraries from large screening decks, commercial compound collections, or virtual databases
Molecular Dynamics Simulation at High Sodium Chloride Concentration: Toward the Inactive Conformation of the Human Adenosine A2A Receptor
The recently solved crystal structure of the human adenosine A2A receptor (hA2AR) shows the characteristics of a partially activated state. Experimental data suggests that high sodium chloride concentration shifts hA2AR to the inactive state. We found that molecular dynamics simulations at high sodium chloride concentration result in an inactive form of hA2AR reflected in the reformation of the “ionic lock” (Arg<sup>102</sup>(3.50)−Glu<sup>228</sup>(6.30)) as well as in the reduction of the αC−αC distance between the intracellular sides of transmembrane helices 3 and 6 (TM3 and TM6). Interestingly, no such stabilization effect was observed at physiological concentrations. Our results suggest that the effect of high sodium chloride concentration might be exploited to generate an inactive state of hA2AR, which is more favorable for identifying pharmacologically relevant antagonists or inverse agonists
Fragment Based Optimization of Metabotropic Glutamate Receptor 2 (mGluR2) Positive Allosteric Modulators in the Absence of Structural Information
Metabotropic glutamate receptor 2
(mGluR2) positive allosteric modulators (PAMs) have been implicated
as potential pharmacotherapy for psychiatric conditions. Screening
our corporate compound deck, we identified a benzotriazole fragment
(<b>4</b>) that was rapidly optimized to a potent and metabolically
stable early lead (<b>16</b>). The highly lipophilic character
of <b>16</b>, together with its limited solubility, permeability,
and high protein binding, however, did not allow reaching of the proof
of concept in vivo. Since further attempts on the optimization of druglike properties
were unsuccessful, the original hit <b>4</b> has been revisited
and was optimized following the principles of fragment based drug
discovery (FBDD). Lacking structural information on the receptor–ligand
complex, we implemented a group efficiency (GE) based strategy and
identified a new fragment like lead (<b>60</b>) with more balanced
profile. Significant improvement achieved on the druglike properties
nominated the compound for in vivo proof of concept studies that revealed
the chemotype being a promising PAM lead targeting mGluR2 receptors